parsimony output changed

[mothur.git] / globaldata.hpp

diff --git a/globaldata.hpp b/globaldata.hpp
index 277d351062fd67726f0ba05d53647d8c98b2a53c..309ab4a09c712132617c1fab8bd96e7849f4643b 100644 (file)
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -1,16 +1,7 @@
 #ifndef GLOBALDATA_HPP
 #define GLOBALDATA_HPP
 
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <iomanip>
-#include <map>
-#include <sstream>
-#include <stdexcept>
-#include <exception>
-
+#include "mothur.h"
 #include "groupmap.h"
 #include "treemap.h"
 
@@ -41,10 +32,9 @@ public:
        TreeMap* gTreemap;
        string inputFileName, helpRequest, commandName;
        bool allLines;
-       vector<string> Estimators; //holds estimators to be used
+       vector<string>  Estimators, Groups; //holds estimators to be used
        set<int> lines; //hold lines to be used
        set<string> labels; //holds labels to be used
-       vector<string> Groups;
        
        string getPhylipFile();
        string getColumnFile();
@@ -65,7 +55,10 @@ public:
        string getIters();
        string getJumble();
        string getFreq();
+       string getAbund();
        string getRandomTree();
+       string getGroups();
+
        void setListFile(string);
        void setPhylipFile(string);
        void setColumnFile(string);
@@ -74,16 +67,22 @@ public:
        void setSabundFile(string);
        void setFormat(string);
        void setRandomTree(string);
+       void setGroups(string);
        void setCalc(string);
 
        
        void setListVector(ListVector*);
        void setSparseMatrix(SparseMatrix*);
+       void clear(); 
+       void clearLabels();
+       void clearAbund();
+       
        void parseGlobalData(string, string);
                
 private:
        string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
-       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc;
+       string cutoff, format, precision, method, fileroot, iters, jumble, freq, calc, abund;
+
        static GlobalData* _uniqueInstance;
        GlobalData( const GlobalData& ); // Disable copy constructor
        void operator=( const GlobalData& ); // Disable assignment operator
@@ -91,7 +90,6 @@ private:
        ~GlobalData();
        ListVector* gListVector;
        SparseMatrix* gSparseMatrix;
-       void clear();  //clears all parameters
        void reset();   //clears all non filename parameters